Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Smad3

Cell type

Cell type Class
Blood
Cell type
CH12
Tissue
Blood
Lineage
cellLine
Description
B-cell lymphoma (GM12878 analog)

Attributes by original data submitter

Sample

source_name
Ch12 cell line
cell type
Ch12 cell line
treatment
treated with TGFb 24h
target
Smad3
experimental type
ChIP-Seq

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10' at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research). ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on Illumina HiSeq 3000.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
50432144
Reads aligned (%)
93.8
Duplicates removed (%)
16.7
Number of peaks
9831 (qval < 1E-05)

mm9

Number of total reads
50432144
Reads aligned (%)
93.7
Duplicates removed (%)
16.7
Number of peaks
9908 (qval < 1E-05)

Base call quality data from DBCLS SRA